My long-term career goal is to become an independent physician-scientist, focused on applying genomic technologies to better understand cancer. This proposal describes a 5 year training program for the development of an academic career in genomics, cancer and Anatomic Pathology. Through this training program, I will gain new skills in genomics and systems biology and their application to human disease. Dr. Kevin White, who is a leader in the field and Director of the Institute for Genomics and Systems Biology, will mentor my scientific development. Dr. Olufunmilayo I. Olopade, a recognized leader in the breast cancer research, will serve as a co-mentor on this project. She is the director of the Center for Clinical Cancer Genetics and Global Health at the University of Chicago Medical Center. In addition, an advisory committee of highly-regarded medical scientists will provide scientific and career advice. The project I have designed is not an extension of existing projects in the White or Olopade lab; rather I have taken the development of novel technologies and the White's labs expertise in generating and analyzing large datasets and merged it with my knowledge of cancer and disease to establish an independent line of research. I plan use genomic techniques to study human tumors extensively in my own independent lab, so the mentored phase of my training in the White lab will provide me with a critical additional training period in which to learn how to apply cutting edge genomic technologies to cancer. I have proposed a 5-year training period during which I will acquire skills necessary to become an independent physician-scientist through interactions with my mentors and participation in formal didactics, national meetings and conferences. I will further develop my scientific skills by pursuing a unique cross-disciplinary research training program in Pathology and Genomics and Systems Biology. In addition to expanding my scientific skill set, I will gain experience in other skills necessary to become a successful independent investigator, such as grant writing, mentoring, and lab management. Furthermore, this additional training will give me time to generate and publish enough data to be competitive for R01 funding. This training will propel the me to an independent investigator position with a deep knowledge of cancer, so that I can make valuable contributions to the cancer field. Breast cancer, the second leading cause of cancer death amongst American women, can be divided into multiple subtypes with different biological behaviors, sensitivity to therapy, and survival. These differences in behavior and treatment sensitivities suggest that the development of subtype-specific therapies will lead to more effective treatment. However, the molecular mechanisms responsible for differences in gene expression, biological behavior, and ultimately outcome, between the different subtypes are poorly understood. We hypothesize that clinically relevant differences between breast cancer subtypes are driven by subtype-specific molecular aberrations. We propose to use RNA sequencing to identify these molecular aberrations. RNA-seq will allow us to analyze several processes, including isoform-specific expression, novel fusion genes, and inherited and somatic genetic variants. Thus, RNA-sequencing will allow me to investigate the role of alternative promoter usage, alterative splicing, chromosomal rearrangements, and inherited and acquired genetic variants in disease heterogeneity in breast cancer. However, unlike most cancer sequencing studies, we will not focus solely on acquired mutations. Given the known role of inherited variants in cancer, and the suspected role of rare alleles in complex disease, we regard both inherited and acquired variants with interest. Indeed, our preliminary studies (see Aim 1 and 2) strongly suggest that we can differentiate two subtypes of breast cancer based on shared genetic variation contained largely in rare deleterious alleles, which include both mutations and inherited variants. Furthermore, our preliminary data suggests that we can differentiate breast cancer subtypes based not only by gene expression, but also by isoform usage alone. Having identified isoforms and genetic variants that distinguish breast cancer subtypes, we will determine if these isoforms or genetic variants alter protein function in cell line models. We will then correlate these effects in human tumor tissue. Thus, through this work we expect to develop a better understanding of the mechanisms underlying shared phenotypic behavior within subtypes of breast cancer. Our contribution here is expected to be the identification of molecular mechanisms, pathways, and processes that differentiate ERBC and TNBC. These mechanisms represent subtype-specific drivers of disease and thus potential targets for therapeutic intervention. By identifying and targeting these mechanisms, we will be able to design more effective, subtype-specific therapies for breast cancer. Furthermore, this work will provide important advances in our understanding of the biology underlying disease heterogeneity. The lessons learned here about the contribution of alternative splicing, fusion-genes, rare, inherited variants and somatic mutations to disease heterogeneity will be applicable to many diseases.